# A Hidden Markov Model Approach for Identifying Differentially Methylated Sites and Regions for Beta-Valued DNA Methylation Data

## Documentation for package ‘betaHMM’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A | Accessors for the betaHMM package.
A-method | Accessors for the betaHMM package.
annotatedData | Accessors for the betaHMM package.
annotatedData-method | Accessors for the betaHMM package.
annotation_data | MethylationEPIC manifest data.
AUC | Accessors for the betaHMM package.
AUC-method | Accessors for the betaHMM package.
betaHMM | HMM for beta valued DNA data
betaHMM-method | HMM for beta valued DNA data
betaHMM-methods | HMM for beta valued DNA data
betaHMMResults | betaHMMResults object and constructor
betaHMMResults-class | betaHMMResults object and constructor
betaHMMrun | The betaHMM model parameter estimation function
chromosome_number | Accessors for the betaHMM package.
chromosome_number-method | Accessors for the betaHMM package.
dmcResults | dmcResults object and constructor
dmcResults-class | dmcResults object and constructor
dmc_identification | DMC identification from estimated betaHMM model parameters
dmc_identification-method | DMC identification from estimated betaHMM model parameters
dmc_identification-methods | DMC identification from estimated betaHMM model parameters
dmc_identification_run | DMC identification from estimated betaHMM model parameters
dmrResults | dmrResults object and constructor
dmrResults-class | dmrResults object and constructor
dmr_identification | DMR identification from DMCs identified
dmr_identification-method | DMR identification from DMCs identified
dmr_identification-methods | DMR identification from DMCs identified
dmr_identification_run | DMR identification from DMCs identified
hidden_states | Accessors for the betaHMM package.
hidden_states-method | Accessors for the betaHMM package.
K | Accessors for the betaHMM package.
K-method | Accessors for the betaHMM package.
llk | Accessors for the betaHMM package.
llk-method | Accessors for the betaHMM package.
model_parameters | Accessors for the betaHMM package.
model_parameters-method | Accessors for the betaHMM package.
N | Accessors for the betaHMM package.
N-method | Accessors for the betaHMM package.
pca_methylation_data | Simulated DNA methylation data
phi | Accessors for the betaHMM package.
phi-method | Accessors for the betaHMM package.
plot | Visualize results from 'betaHMM'/ 'dmc_identification'/ 'threshold_identification' functions.
plot-method | Visualize results from 'betaHMM'/ 'dmc_identification'/ 'threshold_identification' functions.
plot-methods | Visualize results from 'betaHMM'/ 'dmc_identification'/ 'threshold_identification' functions.
R | Accessors for the betaHMM package.
R-method | Accessors for the betaHMM package.
sample_annotation_file | MethylationEPIC manifest data.
sample_methylation_file | Simulated DNA methylation data
summary | Summarize results from the three betaHMM workflow functions
summary-method | Summarize results from the three betaHMM workflow functions
summary-methods | Summarize results from the three betaHMM workflow functions
tau | Accessors for the betaHMM package.
tau-method | Accessors for the betaHMM package.
threshold | Accessors for the betaHMM package.
threshold-method | Accessors for the betaHMM package.
threshold_identification | HMM for beta valued DNA data for a single treatment condition
threshold_identification-method | HMM for beta valued DNA data for a single treatment condition
threshold_identification-methods | HMM for beta valued DNA data for a single treatment condition
threshold_identification_run | Threshold indentification function
threshold_Results | threshold_Results object and constructor
threshold_Results-class | threshold_Results object and constructor
treatment_group | Accessors for the betaHMM package.
treatment_group-method | Accessors for the betaHMM package.
uncertainty | Accessors for the betaHMM package.
uncertainty-method | Accessors for the betaHMM package.